Selecting connected pixels in a binary mask in 3D

Hi all,

I was wondering if anyone knew a way of selecting connected pixels in a binary mask in 3D to allow individual ‘objects’ within a image stack/volume to be selected? So similar to the wand tracing tool in 2D.

At the moment I do have a method of doing this but is quite convoluted: 3DObjectCounter > MapsToShowObject, then colour threshold to isolate my object of interest. This does work but I was wondering if there was another way…

Thoughts?

Dear @Jonny251990,

Could you be more specific about what you are trying to achieve? In any case, selections/ROIs in ImageJ are restricted to one slice/plane as far as I know. However, it sounds like you are looking to generate a binary image from your selection?

Best,
Stefan

Hi,

Maybe you want to have a look to 3DManager :
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start
you can select and manipulate individual objects from a segmented image (that is binary then labelled).

Best,

Thomas

To add two more options to the discussion, you can do that in MorphoLibJ using two consecutive menu commands (as suggested by @ThomasBoudier):

  1. Plugins > MorphoLibJ > Binary Images > Connected Components Labeling to assign a different integer value to each 3D connected region.
  2. Plugins > MorphoLibJ > Label Images > Select Label(s) to create a new image with only the regions whose label number you select.

Or interactively by using Plugins > MorphoLibJ > Interactive Morphological Reconstruction 3D and reconstructing by dilation from the seed point you select:

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